public void testEnhanceDefer() throws IOException {
NetcdfDataset ncd =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissing), -1, null, null);
VariableDS enhancedVar = (VariableDS) ncd.findVariable("t1");
NetcdfDataset ncdefer =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissingDefer), -1, null, null);
VariableDS deferVar = (VariableDS) ncdefer.findVariable("t1");
Array data = enhancedVar.read();
Array dataDefer = deferVar.read();
System.out.printf("Enhanced=");
NCdumpW.printArray(data);
System.out.printf("%nDeferred=");
NCdumpW.printArray(dataDefer);
System.out.printf("%nProcessed=");
CompareNetcdf2 nc = new CompareNetcdf2(new Formatter(System.out), false, false, true);
assert !nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
IndexIterator ii = dataDefer.getIndexIterator();
while (ii.hasNext()) {
double val = deferVar.convertScaleOffsetMissing(ii.getDoubleNext());
ii.setDoubleCurrent(val);
}
NCdumpW.printArray(dataDefer);
assert nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
ncd.close();
ncdefer.close();
}
@Test
public void testFloatingPointCompare() throws Exception {
String spec =
TestDir.cdmUnitTestDir + "ft/fmrc/fp_precision/sediment_thickness_#yyMMddHHmm#.*\\.nc$";
System.out.printf("%n====================FMRC dataset %s%n", spec);
Formatter errlog = new Formatter();
Fmrc fmrc = Fmrc.open(spec, errlog);
assert (fmrc != null) : errlog;
try (ucar.nc2.dt.GridDataset gridDs = fmrc.getDatasetBest()) {
GridDatatype v = gridDs.findGridByShortName("thickness_of_sediment");
assert v != null;
GridCoordSystem gcs = v.getCoordinateSystem();
CoordinateAxis1DTime time = gcs.getTimeAxis1D();
Assert.assertEquals("hours since 2015-03-08 12:51:00.000 UTC", time.getUnitsString());
Assert.assertEquals(74, time.getSize());
Array data = time.read();
System.out.printf("%s%n", NCdumpW.toString(data));
for (CalendarDate cd : time.getCalendarDates()) {
assert cd.getFieldValue(CalendarPeriod.Field.Minute) == 0 : System.out.printf("%s%n", cd);
}
}
}
private void showDeclaration(BeanTableSorted from, boolean isNcml) {
Variable v = getCurrentVariable(from);
if (v == null) return;
infoTA.clear();
if (isNcml) {
Formatter out = new Formatter();
try {
NCdumpW.writeNcMLVariable(v, out);
} catch (IOException e) {
e.printStackTrace();
}
infoTA.appendLine(out.toString());
} else {
infoTA.appendLine(v.toString());
}
if (Debug.isSet("Xdeveloper")) {
infoTA.appendLine("\n");
infoTA.appendLine("FULL NAME = " + v.getFullName());
infoTA.appendLine("\n");
infoTA.appendLine(v.toStringDebug());
}
infoTA.gotoTop();
infoWindow.setTitle("Variable Info");
infoWindow.show();
}
/*
Structure {
int a_name;
byte b_name(3);
byte c_name(3);
short d_name(3);
int e_name(3);
long f_name(3);
int g_name(3);
short h_name(3);
int i_name(3);
long j_name(3);
float k_name(3);
double l_name(3);
} CompoundNative(15);
type = Layout(8); type= 1 (contiguous) storageSize = (15,144) dataSize=0 dataAddress=2048
*/
@Test
public void testReadH5StructureArrayMembers() throws java.io.IOException {
try (NetcdfFile ncfile = TestH5.openH5("complex/compound_native.h5")) {
Variable dset = ncfile.findVariable("CompoundNative");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 15);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 15);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testReadH5StructureArrayMembers ok");
}
public String getValue() {
Array value = att.getValues();
try {
return NCdumpW.printArray(value, null, null);
} catch (IOException e) {
return e.getMessage();
}
}
public void testStride(String stride) throws IOException, InvalidRangeException {
Variable time = ncfile.findVariable("time");
ArrayInt all = (ArrayInt) time.read();
ArrayInt correct = (ArrayInt) all.section(new Section(stride).getRanges());
System.out.printf("correct(%s) %s", stride, NCdumpW.toString(correct));
ArrayInt data = (ArrayInt) time.read(stride);
System.out.printf("data(%s) %s%n", stride, NCdumpW.toString(data));
Index ci = correct.getIndex();
Index di = data.getIndex();
for (int i = 0; i < data.getSize(); i++)
assert (data.getInt(di.set(i)) == correct.getInt(ci.set(i)))
: stride
+ " index "
+ i
+ " = "
+ data.getInt(di.set(i))
+ " != "
+ correct.getInt(ci.set(i));
}
private void showValueDiffs(CoordinateAxis axis) {
if (!axis.isNumeric()) return;
try {
if (axis instanceof CoordinateAxis1D) {
CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
double[] mids = axis1D.getCoordValues();
double[] diffs = new double[mids.length];
for (int i = 0; i < mids.length - 1; i++) diffs[i] = mids[i + 1] - mids[i];
printArrays("midpoint differences", mids, diffs);
} else if (axis instanceof CoordinateAxis2D) {
CoordinateAxis2D axis2D = (CoordinateAxis2D) axis;
ArrayDouble.D2 mids = axis2D.getCoordValuesArray();
int[] shape = mids.getShape();
ArrayDouble.D2 diffx =
(ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0], shape[1] - 1});
for (int j = 0; j < shape[0]; j++) {
for (int i = 0; i < shape[1] - 1; i++) {
double diff = mids.get(j, i + 1) - mids.get(j, i);
diffx.set(j, i, diff);
}
}
infoTA.appendLine(NCdumpW.toString(diffx, "diff in x", null));
ArrayDouble.D2 diffy =
(ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0] - 1, shape[1]});
for (int j = 0; j < shape[0] - 1; j++) {
for (int i = 0; i < shape[1]; i++) {
double diff = mids.get(j + 1, i) - mids.get(j, i);
diffy.set(j, i, diff);
}
}
infoTA.appendLine("\n\n\n");
infoTA.appendLine(NCdumpW.toString(diffy, "diff in y", null));
}
} catch (Exception e1) {
e1.printStackTrace();
infoTA.appendLine(e1.getMessage());
}
}
String ncdumpmetadata(NetcdfDataset ncfile) throws Exception {
StringWriter sw = new StringWriter();
// Print the meta-databuffer using these args to NcdumpW
try {
if (!ucar.nc2.NCdumpW.print(ncfile, "-unsigned", sw, null))
throw new Exception("NcdumpW failed");
} catch (IOException ioe) {
throw new Exception("NcdumpW failed", ioe);
}
sw.close();
return sw.toString();
}
private void showValues(CoordinateAxis axis) {
try {
if (axis instanceof CoordinateAxis1D && axis.isNumeric()) {
CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
printArray("midpoints=", axis1D.getCoordValues());
if (!axis1D.isInterval()) {
printArray("edges=", axis1D.getCoordEdges());
} else {
printArray("bound1=", axis1D.getBound1());
printArray("bound2=", axis1D.getBound2());
Formatter f = new Formatter();
double[] mid = axis1D.getCoordValues();
double[] b1 = axis1D.getBound1();
double[] b2 = axis1D.getBound2();
for (int i = 0; i < b1.length; i++) {
f.format("%f (%f,%f) = %f%n", mid[i], b1[i], b2[i], b2[i] - b1[i]);
}
infoTA.appendLine(f.toString());
}
} else if (axis instanceof CoordinateAxis2D && axis.isNumeric()) {
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
showValues2D((CoordinateAxis2D) axis);
} else {
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
}
} catch (IOException e1) {
e1.printStackTrace();
infoTA.appendLine(e1.getMessage());
}
}
String ncdumpdata(NetcdfDataset ncfile) throws Exception {
StringWriter sw = new StringWriter();
// Dump the databuffer
sw = new StringWriter();
try {
if (!ucar.nc2.NCdumpW.print(ncfile, "-vall -unsigned", sw, null))
throw new Exception("NCdumpW failed");
} catch (IOException ioe) {
ioe.printStackTrace();
throw new Exception("NCdumpW failed", ioe);
}
sw.close();
return sw.toString();
}
// test offset only gets applied once
public void testWrapOnce() throws IOException {
String filename = TestAll.cdmUnitTestDir + "ncml/coords/testCoordScaling.ncml";
System.out.printf("%s%n", filename);
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
Variable v = ncd.findCoordinateAxis("Longitude");
assert v != null;
assert v instanceof CoordinateAxis1D;
// if offset is applied twice, the result is not in +-180 range
Array data = v.read();
NCdumpW.printArray(data);
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
assert Math.abs(ii.getDoubleNext()) < 180 : ii.getDoubleCurrent();
}
}
@Test
public void testH5StructureDS() throws java.io.IOException {
int a_name = 0;
String[] b_name =
new String[] {
"A fight is a contract that takes two people to honor.",
"A combative stance means that you've accepted the contract.",
"In which case, you deserve what you get.",
" -- Professor Cheng Man-ch'ing"
};
String c_name = "Hello!";
// H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
try (NetcdfDataset ncfile =
NetcdfDataset.openDataset(TestH5.testDir + "complex/compound_complex.h5")) {
Variable dset = ncfile.findVariable("CompoundComplex");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 6);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 6);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
assert sd.getScalarInt("a_name") == a_name;
a_name++;
assert sd.getScalarString("c_name").equals(c_name);
String[] results = sd.getJavaArrayString(sd.findMember("b_name"));
assert results.length == b_name.length;
int count = 0;
for (String r : results) assert r.equals(b_name[count++]);
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testH5StructureDS ok");
}
private void showValuesAsDates(CoordinateAxis axis) {
String units = axis.getUnitsString();
String cal = getCalendarAttribute(axis);
CalendarDateUnit cdu = CalendarDateUnit.of(cal, units);
try {
infoTA.appendLine(units);
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
if (axis.getDataType().isNumeric()) {
if (axis instanceof CoordinateAxis2D) {
showDates2D((CoordinateAxis2D) axis, cdu);
} else if (axis instanceof CoordinateAxis1D) { // 1D
showDates1D((CoordinateAxis1D) axis, cdu);
} else { // > 2D
Array data = axis.read();
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
double val = ii.getDoubleNext();
infoTA.appendLine(makeCalendarDateStringOrMissing(cdu, val));
}
}
} else { // must be iso dates
Array data = axis.read();
Formatter f = new Formatter();
if (data instanceof ArrayChar) {
ArrayChar dataS = (ArrayChar) data;
ArrayChar.StringIterator iter = dataS.getStringIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
} else if (data instanceof ArrayObject) {
IndexIterator iter = data.getIndexIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
}
}
} catch (Exception ex) {
ex.printStackTrace();
infoTA.appendLine(ex.getMessage());
}
}
public String getValue() {
Array value = att.getValues();
return NCdumpW.toString(value, null, null);
}